active-enhancers

Identifying active enhancers and well known transcription factor binding sites from GRO-seq data.

This a fork of Kraus-Lab/active-enhancers, rewritten to use Nextflow to streamline the use.

Running

Install Nextflow and Docker

nextflow run Functional-Genomics-Lab/active-enhancers -profile utd_ganymede

Results

Results of the reproduction can be viewed on Hugging Face

Original Authors

• Anusha Nagari
• Venkat Malladi

Included tools and software

These are all built and installed via Wave containers

• R 3.0.2
• Python 2.7.2
• Perl v5.18.2
• fastqc 0.10.1
• cutadapt 1.2.1
• BWA 0.7.12
• samtools 0.1.19
• bedtools 2.17.0
• groHMM
• SRA Tools 2.5.4

Data

Data for the tutorial is downloaded from GSE43835.

This experiment looks at GRO-seq data from MCF-7 human breast cancer cells in response to short time course of E2 treatment (10min, 40min) and no treatment (Vehicle).